Physiology and Molecular Biology of Plants

, Volume 23, Issue 3, pp 629–640 | Cite as

Genome-wide identification, phylogeny and expression analyses of SCARECROW-LIKE(SCL) genes in millet (Setaria italica)

  • Hongyun Liu
  • Jiajia Qin
  • Hui Fan
  • Jinjin Cheng
  • Lin Li
  • Zheng LiuEmail author
Research Article


As a member of the GRAS gene family, SCARECROW-LIKE (SCL) genes encode transcriptional regulators that are involved in plant information transmission and signal transduction. In this study, 44 SCL genes including two SCARECROW genes in millet were identified to be distributed on eight chromosomes, except chromosome 6. All the millet genes contain motifs 6–8, indicating that these motifs are conserved during the evolution. SCL genes of millet were divided into eight groups based on the phylogenetic relationship and classification of Arabidopsis SCL genes. Several putative millet orthologous genes in Arabidopsis, maize and rice were identified. High throughput RNA sequencing revealed that the expressions of millet SCL genes in root, stem, leaf, spica, and along leaf gradient varied greatly. Analyses combining the gene expression patterns, gene structures, motif compositions, promoter cis-elements identification, alternative splicing of transcripts and phylogenetic relationship of SCL genes indicate that the these genes may play diverse functions. Functionally characterized SCL genes in maize, rice and Arabidopsis would provide us some clues for future characterization of their homologues in millet. To the best of our knowledge, this is the first study of millet SCL genes at the genome wide level. Our work provides a useful platform for functional analysis of SCL genes in millet, a model crop for C4 photosynthesis and bioenergy studies.


Setaria italica GRAS family SCARECROW-LIKE (SCL) genes Bioinformatics Gene expression patterns 



We thank the Natural Science Foundation of Hebei Province (No. C2015201176), the Scientific Research Foundation for the Returned Overseas Chinese Scholars by State Education Ministry of China (No. 2011–1139), the Postgraduate Research Innovation Fund Project of Hebei Province (S201622) for funding.

Author contributions

HL performed the experiments, analyzed the data and wrote the manuscript; JQ, HF, JC, LL participated in analyzing data; ZL conceived the study, analyzed the data and revised the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

12298_2017_455_MOESM1_ESM.jpg (380 kb)
Suppl. 1 Sequence logos of subgroups of VHIID signature motifs in millet generated by MEME. The signature amino acids of VHIID were marked by red dot. The number on X axis represents the positions in SCL conserved motifs. The number on y axis represents information content measured in bits. (A: motif 7; B: motif 2; C: motif 11) (JPEG 379 kb)
12298_2017_455_MOESM2_ESM.jpg (617 kb)
Suppl. 2 Sequence logos of subgroups of PFTRE signature motifs in millet generated by MEME. The signature amino acids of PFTRE was marked by red dot. The absolutely conserved amino acids beyond the signature amino acids was marked by blue dot. The number on X axis represents the positions in SCL conserved motifs. The number on Y axis represents information content measured in bits. (A: motif 10; B: motif 8; C: motif 3; D: motif 12) (JPEG 617 kb)
12298_2017_455_MOESM3_ESM.jpg (393 kb)
Suppl. 3 Sequence logos of subgroups of SAW signature motifs in millet generated by MEME. The signature amino acids of SAW was marked by red dot. The number on X axis represents the positions in SCL conserved motifs. The number on Y axis represents information content measured in bits. (A: motif 1; B: motif 4) (JPEG 392 kb)
12298_2017_455_MOESM4_ESM.jpg (115 kb)
Suppl. 4 Locations of SCL genes on chromosomes of Arabidopsis (JPEG 115 kb)
12298_2017_455_MOESM5_ESM.jpg (215 kb)
Suppl. 5 Locations of SCL genes on chromosomes of maize (JPEG 214 kb)
12298_2017_455_MOESM6_ESM.jpg (183 kb)
Suppl. 6 Gene structures of the Arabidopsis SCL genes (JPEG 183 kb)
12298_2017_455_MOESM7_ESM.jpg (284 kb)
Suppl. 7 Gene structures of the maize SCL genes (JPEG 283 kb)
12298_2017_455_MOESM8_ESM.jpg (74 kb)
Suppl. 8 Alternative splicing transcripts of Si034417m.g and Si035052m.g (A: Tanscripts of Si034417m.g; B: Tanscripts of Si035052m.g) (JPEG 73 kb)
12298_2017_455_MOESM9_ESM.docx (53 kb)
Suppl. 9 The promoter cis-acting elements of SCL genes in millet (DOCX 53 kb)
12298_2017_455_MOESM10_ESM.jpg (2.5 mb)
Suppl. 10 Nucleotide coding sequence alignment between Seita.7G305500 and Seita.8G008700 by Clustal X (1.81) (JPEG 2524 kb)
12298_2017_455_MOESM11_ESM.jpg (741 kb)
Suppl. 11 Peptide sequence alignment between Seita.7G305500 and Seita.8G008700 by Clustal X (1.81) (JPEG 741 kb)


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Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2017

Authors and Affiliations

  1. 1.College of Life SciencesHebei UniversityBaodingPeople’s Republic of China
  2. 2.School of Physical SciencesUniversity of the Chinese Academy of SciencesBeijingPeople’s Republic of China
  3. 3.College of BiologyHunan UniversityChangshaPeople’s Republic of China

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